This article develops the existing literature on the challenges facing the Ugandan refugee protection system by showing the interrelatedness of these challenges and linking them to the core assumptions of the “Uganda Model” of refugee protection. To that effect, it presents primary, qualitative data gathered in the field. This empirical evidence reveals profound marginalisation of refugees within Uganda and the difficulties of the authorities to remedy it in the face of the status quo, where the international community’s support has been disproportionately small. This reality, being strikingly at odds with the promise of Uganda’s refugee protection architecture, has led the government and UNHCR officials who were interviewed for this research to doubt whether it is possible to uphold this architecture. This, together with the outcomes of a desk study utilising existing quantitative and qualitative data, suggests that the Uganda Model might, at the time of writing, be approaching its threshold of viability. The findings suggest that a substantial rethink of the model’s assumptions might be in order.